Code from fileio.Rmd vignette for unit tests

[GegznaV]

This issue is to continue discussion that started as:

• Code from fileio.Rmd vignette for unit tests cbeleites/hyperSpec#174

The original message:

---

This is the code from fileio.Rmd which could be used to create unit tests: fileio-for-unit-tests.zip as stated in

• Translate vignettes from Sweave to R Markdown cbeleites/hyperSpec#79 (comment):

untangle historic mix with unit tests into vignette and unit tests

---

The contents of 'fileio-for-unit-tests.zip':

# ============================================================================
# =========== R code extracted from fileio.Rmd vignette ======================
# ============================================================================


## ----setup-io, include=FALSE---------------------------------------------------------
# Packages -------------------------------------------------------------------
library(hyperSpec)
library(R.matlab)

## ----array---------------------------------------------------------------------------
data <- array(1:24, 4:2)
wl <- c(550, 630)
x <- c(1000, 1200, 1400)
y <- c(1800, 1600, 1400, 1200)
data

## ----array-import--------------------------------------------------------------------
d <- dim(data)
dim(data) <- c(d[1] * d[2], d[3])

x <- rep(x, each = d[1])
y <- rep(y, d[2])

spectra <- new("hyperSpec",
  spc = data,
  data = data.frame(x, y), wavelength = wl
)

## ------------------------------------------------------------------------------------
y <- seq_len(d[1])
x <- seq_len(d[2])

## ----readcollapse--------------------------------------------------------------------
files <- Sys.glob("fileio/spc.Kaisermap/*.spc")
files <- files[seq(1, length(files), by = 2)] # import low wavenumber region only
spc <- lapply(files, read.spc)
length(spc)
spc[[1]]
spc <- collapse(spc)
spc


## ----read.txt.t----------------------------------------------------------------------
file <- read.table("fileio/txt.t/Triazine 5_31.txt", header = TRUE, dec = ",", sep = "\t")

triazine <- new("hyperSpec",
  wavelength = file[, 1], spc = t(file[, -1]),
  data = data.frame(sample = colnames(file[, -1])),
  labels = list(
    .wavelength = expression(2 * theta / degree),
    spc = "I / a.u."
  )
)
triazine

## ----plot-triazine, fig.cap=CAPTION--------------------------------------------------
plot(triazine[1])

## ------------------------------------------------------------------------------------
read.jdx("fileio/jcamp-dx/shimadzu.jdx", encoding = "latin1", keys.hdr2data = TRUE)
read.jdx("fileio/jcamp-dx/virgilio.jdx")

## ------------------------------------------------------------------------------------
read.jdx("fileio/jcamp-dx/virgilio.jdx", ytol = 1e-9)


## ----nist-aes------------------------------------------------------------------------
file <- readLines("fileio/NIST/mercurytable2.htm")
# file <- readLines("http://physics.nist.gov/PhysRefData/Handbook/Tables/mercurytable2.htm")

file <- file[-(1:grep("Intensity.*Wavelength", file) - 1)]
file <- file[1:(grep("</pre>", file) [1] - 1)]
file <- gsub("<[^>]*>", "", file)
file <- file[!grepl("^[[:space:]]+$", file)]

colnames <- file[1]
colnames <- gsub("[[:space:]][[:space:]]+", "\t", file[1])
colnames <- strsplit(colnames, "\t")[[1]]
if (!all(colnames == c("Intensity", "Wavelength (&Aring;)", "Spectrum", "Ref. "))) {
  stop("file format changed!")
}

tablestart <- grep("^[[:blank:]]*[[:alpha:]]+$", file) + 1
tableend <- c(tablestart[-1] - 2, length(file))
tables <- list()
for (t in seq_along(tablestart)) {
  tmp <- file[tablestart[t]:tableend[t]]
  tables[[t]] <- read.fwf(textConnection(tmp), c(5, 8, 12, 15, 9))
  colnames(tables[[t]]) <- c("Intensity", "persistent", "Wavelength", "Spectrum", "Ref. ")
  tables[[t]]$type <- gsub("[[:space:]]", "", file[tablestart[t] - 1])
}
tables <- do.call(rbind, tables)
levels(tables$Spectrum) <- gsub(" ", "", levels(tables$Spectrum))

Hg.AES <- list()
for (s in levels(as.factor(tables$Spectrum))) {
  Hg.AES[[s]] <- new("hyperSpec",
    wavelength = tables$Wavelength[tables$Spectrum == s],
    spc = tables$Intensity[tables$Spectrum == s],
    data = data.frame(Spectrum = s),
    label = list(
      .wavelength = expression(lambda / ring(A)),
      spc = "I"
    )
  )
}

## ----plot-hg-aes, fig.cap=CAPTION----------------------------------------------------
plot(collapse(Hg.AES), lines.args = list(type = "h"), col = 1:2)


## ------------------------------------------------------------------------------------
library(R.matlab)


## ----eval=FALSE----------------------------------------------------------------------
## **V. Gegznas's notes**:
## FIXME:`file `spectra.mat` is not present.
spc.mat <- readMat("fileio/spectra.mat")


## ----eval=FALSE----------------------------------------------------------------------
## **V. Gegznas's notes**:
## FIXME: there are issues in downloading `Rcompression` package as omegahat.org
## does not update as quickly as a new version of R is released.
install.packages("Rcompression", repos = "http://www.omegahat.org/R")

## ----read.mat.Cytospec-blocks--------------------------------------------------------
read.mat.Cytospec("fileio/mat.cytospec/cytospec.mat", blocks = TRUE)


## ----read.mat.Cytospec---------------------------------------------------------------
read.mat.Cytospec("fileio/mat.cytospec/cytospec.mat", blocks = 1)


## ----read.ENVI-----------------------------------------------------------------------
spc <- read.ENVI("fileio/ENVI/example2.img")
spc

## ------------------------------------------------------------------------------------
read.spc("fileio/spc.Kaisermap/ebroAVII.spc", keys.hdr2data = TRUE)

## ------------------------------------------------------------------------------------
read.spc("fileio/spc.Kaisermap/ebroAVII.spc", keys.log2data = TRUE)

## ----read.spc.list-old---------------------------------------------------------------
barbiturates <- read.spc("fileio/spc/BARBITUATES.SPC")

## ------------------------------------------------------------------------------------
class(barbiturates)

## ------------------------------------------------------------------------------------
length(barbiturates)

## ------------------------------------------------------------------------------------
barbiturates <- collapse(barbiturates, collapse.equal = FALSE)
barbiturates

## ------------------------------------------------------------------------------------
barbiturates[[1:10, , 25 ~ 30]]


## ----eval=FALSE----------------------------------------------------------------------
header <- list(
  samples = 64 * no.images.in.row,
  lines = 64 * no.images.in.column,
  bands = no.data.points.per.spectrum,
  `data type` = 4,
  interleave = "bip"
)


## ----readENVINicolet-----------------------------------------------------------------
spc <- read.ENVI.Nicolet("fileio/ENVI/example2.img", nicolet.correction = TRUE)
spc ## dummy sample with all intensities zero


## ----Kaiser.txt.comma----------------------------------------------------------------
## 1. import as character
tmp <- scan("fileio/txt.Kaiser/test-lo-4.txt", what = rep("character", 4), sep = ",")
tmp <- matrix(tmp, nrow = 4)

## 2. concatenate every two columns by a dot
wl <- apply(tmp[1:2, ],  2, paste, collapse = ".")
spc <- apply(tmp[3:4, ], 2, paste, collapse = ".")

## 3. convert to numeric and create hyperSpec objectne, though).
spc <- new("hyperSpec", spc = as.numeric(spc), wavelength = as.numeric(wl))
spc


## ----readspcKaiserMap----------------------------------------------------------------
files <- Sys.glob("fileio/spc.Kaisermap/*.spc")
spc.low  <- read.spc.KaiserMap(files[seq(1, length(files), by = 2)])
spc.high <- read.spc.KaiserMap(files[seq(2, length(files), by = 2)])
wl(spc.high) <- wl(spc.high) + 1340
spc


## ----read.txt.Renishaw---------------------------------------------------------------
paracetamol <- read.txt.Renishaw("fileio/txt.Renishaw/paracetamol.txt", "spc")
paracetamol


## ------------------------------------------------------------------------------------
read.txt.Renishaw("fileio/txt.Renishaw/laser.txt.gz", data = "ts")


## ----read.txt.Renishaw-file----------------------------------------------------------
read.txt.Renishaw("fileio/txt.Renishaw/chondro.txt", nlines = 1e5, nspc = 875)


## ----read.txt.Renishaw-compressed, results='hide'------------------------------------
read.txt.Renishaw("fileio/txt.Renishaw/chondro.gz")
read.txt.Renishaw("fileio/txt.Renishaw/chondro.xz")
read.txt.Renishaw("fileio/txt.Renishaw/chondro.lzma")
read.txt.Renishaw("fileio/txt.Renishaw/chondro.gz")
read.txt.Renishaw("fileio/txt.Renishaw/chondro.bz2")
read.zip.Renishaw("fileio/txt.Renishaw/chondro.zip")


## ----Horiba--------------------------------------------------------------------------
spc <- read.txt.Horiba("fileio/txt.HoribaJobinYvon/ts.txt",
  cols = list(
    t = "t / s", spc = "I / a.u.",
    .wavelength = expression(Delta * tilde(nu) / cm^-1)
  )
)
spc


## ----testHoriba-1--------------------------------------------------------------------
spc <- read.txt.Horiba.xy("fileio/txt.HoribaJobinYvon/map.txt")
if (any(dim(spc) != c(141, 4, 616)) ||
  any(abs(spc) < .Machine$double.eps^.5) ||
  is.null(spc$x) || any(is.na(spc$x)) ||
  is.null(spc$y) || any(is.na(spc$y)) ||
  length(setdiff(wl(spc), 1:616)) == 0L) {
  stop("error in testing read.txt.Horiba.xy. Please contact ", maintainer("hyperSpec"))
}
spc


## ----testHoriba-2--------------------------------------------------------------------
spc <- read.txt.Horiba.t("fileio/txt.HoribaJobinYvon/ts.txt")
if (any(dim(spc) != c(100, 3, 1024)) ||
  is.null(spc$t) || any(is.na(spc$t)) ||
  length(setdiff(wl(spc), 1:1024)) == 0L) {
  stop("error in testing read.txt.Horiba.xy. Please contact ", maintainer("hyperSpec"))
}
spc
rm(spc)


## ------------------------------------------------------------------------------------
read.asc.Andor("fileio/asc.Andor/ASCII-Andor-Solis.asc")


## ----witec-spc, results='hide'-------------------------------------------------------
read.spc("fileio/spc.Witec/Witec-timeseries.spc")
read.spc("fileio/spc.Witec/Witec-Map.spc")


## ----witec-dat, results='hide'-------------------------------------------------------
read.dat.Witec("fileio/txt.Witec/Witec-timeseries-x.dat")
read.dat.Witec(
  filex = "fileio/txt.Witec/Witec-Map-x.dat",
  points.per.line = 5, lines.per.image = 5, type = "map"
)


## ----witec-txt, include=FALSE--------------------------------------------------------
read.txt.Witec("fileio/txt.Witec/Witec-timeseries_no.txt")


## ----witec-txt-textfiles, include=FALSE----------------------------------------------
headline <- c(
  "with exported labels and units headerlines:",
  "\nwith exported labels headerline:",
  "\nwith exported units headerline:",
  "\nwithout headerline:"
)
files <- c(
  "fileio/txt.Witec/Witec-timeseries_full.txt",
  "fileio/txt.Witec/Witec-timeseries_label.txt",
  "fileio/txt.Witec/Witec-timeseries_unit.txt",
  "fileio/txt.Witec/Witec-timeseries_no.txt"
)

for (f in seq_along(files)) {
  cat(headline[f], "\n")
  tmp <- format(as.matrix(read.table(files[f], sep = "\t")[1:4, 1:3]))
  apply(tmp, 1, function(l) cat(l, "\n"))
}


## ----witec-txt-map, include=FALSE----------------------------------------------------
read.txt.Witec("fileio/txt.Witec/Witec-Map_full.txt",
  type = "map", hdr.label = TRUE, hdr.units = TRUE)

read.txt.Witec("fileio/txt.Witec/Witec-Map_label.txt",
  type = "map", hdr.label = TRUE, hdr.units = FALSE)

read.txt.Witec("fileio/txt.Witec/Witec-Map_unit.txt",
  type = "map", hdr.label = FALSE, hdr.units = TRUE)

read.txt.Witec("fileio/txt.Witec/Witec-Map_unit.txt",
  type = "map", hdr.label = FALSE, hdr.units = TRUE,
  points.per.line = 5
)

read.txt.Witec("fileio/txt.Witec/Witec-Map_no.txt",
  type = "map", hdr.label = FALSE, hdr.units = FALSE)

read.txt.Witec("fileio/txt.Witec/Witec-Map_no.txt",
  type = "map", hdr.label = FALSE, hdr.units = FALSE,
  lines.per.image = 5
)

read.txt.Witec("fileio/txt.Witec/Witec-Map_no.txt",
  type = "map", hdr.label = FALSE, hdr.units = FALSE,
  points.per.line = 5, lines.per.image = 5
)


## ----witec-txt-Graph, results='hide'-------------------------------------------------
read.txt.Witec.Graph("fileio/txt.Witec/Witec-timeseries (Header).txt")
read.txt.Witec.Graph("fileio/txt.Witec/Witec-Map (Header).txt", type = "map")
read.txt.Witec.Graph("fileio/txt.Witec/nofilename (Header).txt", encoding = "latin1")


## ----comment="", eval=TRUE, echo=FALSE, class.output="add-border sourceCode r"-------
writeLines(readLines("read.txt.PerkinElmer.R"))

## ----read.txt.PerkinElmer, message=FALSE---------------------------------------------
source("read.txt.PerkinElmer.R")
read.txt.PerkinElmer(Sys.glob("fileio/txt.PerkinElmer/flu?.txt"), skip = 54)

---

Please, close tis issue when it gets not relevant.